Do I need all three systems (ELN, LIMS, and LIS)?

Most labs do not need all three. Research and pharma labs typically use an ELN paired with a LIMS. Clinical and diagnostic labs rely on a LIS, sometimes with a LIMS for complex workflows. Only large academic medical centers with both research and clinical operations commonly deploy all three systems.

ELN vs LIMS vs LIS: Which Lab Software Do You Need?

Q: How do ELN, LIMS, and LIS systems integrate with each other?

These systems integrate through APIs, HL7/FHIR interfaces, and middleware. Common integrations include ELN-to-LIMS for pushing experimental results into sample records, LIMS-to-LIS for transferring sample data to clinical workflows, and LIS-to-EMR for reporting patient results. Integration complexity varies by vendor and deployment model.

Q: What about SDMS and CDS — are those different too?

Yes. A Scientific Data Management System (SDMS) focuses on storing and organizing raw instrument data files (chromatograms, spectra, images). A Chromatography Data System (CDS) is specialized for managing chromatographic instrument runs and data analysis. Both are complementary to ELN, LIMS, and LIS rather than replacements.

Q: How much does each system typically cost?

Costs vary widely. Cloud-based ELNs start around $150-300/user/month. LIMS implementations range from $50,000 for small labs to $500,000+ for enterprise deployments. LIS systems for clinical labs typically cost $100,000-$1M+ depending on scale and integrations. Managed services can reduce upfront costs by spreading them over time.

The definitive three-way comparison of Electronic Lab Notebooks, Laboratory Information Management Systems, and Laboratory Information Systems — and when you need more than one.

Trusted by leading diagnostic labs and life sciences companies

Three Systems, Three Different Purposes

ELN, LIMS, and LIS are often confused, but each system serves a fundamentally different role in the laboratory. Understanding these differences is critical before investing in lab informatics.

ELN

Electronic Lab Notebook

Experiment-Centric

A digital replacement for paper lab notebooks. Captures experimental procedures, observations, raw data, and conclusions. The primary tool for documenting research and protecting intellectual property.

Core Capabilities:

Document experiments & protocols
Real-time collaboration
Data capture & visualization
IP & patent documentation
Version-controlled records

Best For:

R&D labs, pharma discovery, academic research, biotech startups

LIMS

Lab Information Management System

Sample-Centric

Manages samples from receipt through testing to disposal. Tracks workflows, automates processes, manages inventory, and ensures quality control across the entire sample lifecycle.

Core Capabilities:

Sample tracking & chain of custody
Workflow & batch processing
Inventory & reagent management
Quality control & assurance
Instrument integration

Best For:

QC labs, environmental testing, pharma manufacturing, food & beverage

LIS

Laboratory Information System

Patient-Centric

Manages clinical laboratory operations with a focus on patient data. Handles test ordering, specimen processing, result reporting, EMR integration, and billing for diagnostic laboratories.

Core Capabilities:

Patient data & demographics
Test ordering & result reporting
EMR/EHR integration (HL7, FHIR)
Billing & insurance processing
Regulatory compliance (CLIA/CAP)

Best For:

Hospital labs, clinical reference labs, pathology, blood banks

In short: ELNs document what you did (experiments). LIMS track what you have (samples). LIS manage who it's for (patients).

Feature-by-Feature Comparison

A detailed look at 18 key capabilities across all three systems. Green means full support, amber means partial or limited support, and gray means not supported.

Feature	ELN	LIMS	LIS
Experiment documentation
Sample/specimen tracking
Patient data management
Workflow automation
Inventory management
Protocol management
EMR/EHR integration
Billing integration
Batch processing
Real-time collaboration
Instrument integration
Audit trail
Chain of custody
Regulatory compliance
Data visualization & analysis
IP & patent documentation
Test ordering & requisitions
Environmental monitoring

Full support Partial support Not supported

Which System Is Right for Your Lab?

The right system depends on your lab type, workflows, and regulatory requirements. Here is a quick decision guide.

Research & Pharma Labs

ELN+LIMS

Use an ELN for experiment documentation and IP protection. Add a LIMS for sample management, inventory tracking, and QC workflows. This combination covers discovery through development.

Clinical & Diagnostic Labs

LIS+ optionalLIMS

A LIS is essential for patient data, test ordering, result reporting, and billing. Add a LIMS if you have complex sample workflows, high-volume batch processing, or need detailed chain of custody tracking.

Environmental & Testing Labs

LIMS

A LIMS is your primary system. It handles sample intake, testing workflows, chain of custody, regulatory compliance, and reporting. Most environmental labs do not need an ELN or LIS.

Hospital Labs & Academic Medical Centers

LIS+ELN

The clinical lab needs a LIS for patient workflows and EMR integration. Research departments benefit from an ELN for experiment documentation. Large operations may also add a LIMS for the analytical core.

Common System Combinations

Most laboratories need more than one system. Here are the most common pairings and why they work together.

ELN + LIMS

The standard combination for research and pharmaceutical labs. Scientists use the ELN to design and document experiments while the LIMS manages samples, inventory, and QC workflows.

Typical users: Pharma R&D, biotech, chemical companies, contract research organizations

LIMS + LIS

Common in large clinical operations that process both routine patient specimens and complex analytical testing. The LIS handles patient workflows and the LIMS manages high-throughput sample processing.

Typical users: Reference labs, large hospital networks, national testing labs

All Three: ELN + LIMS + LIS

Reserved for academic medical centers and large organizations with both clinical and research missions. Requires careful integration planning and dedicated informatics support.

Typical users: University hospitals, NIH-funded research centers, integrated health systems

Integration Is Key

When deploying multiple systems, integration between them is critical. Common integration points include:

ELN to LIMS: Push experimental results into sample records
LIMS to LIS: Transfer sample data to clinical workflows
LIS to EMR: Report patient results to electronic medical records
LIMS to instruments: Automate data capture from analytical equipment
ELN to LIMS: Share protocols and standard operating procedures
LIS to billing: Automate charge capture and insurance claims

Explore Related Resources

LIMS vs LIS

Deep dive into the differences between LIMS and LIS for laboratory operations.

What Is a LIMS?

Complete guide to Laboratory Information Management Systems and their capabilities.

What Is a LIS?

Everything you need to know about Laboratory Information Systems for clinical labs.

LIMS Glossary

Key terms and definitions for Laboratory Information Management Systems.

LIS Glossary

Essential terminology for Laboratory Information Systems and clinical informatics.

LIMS Consulting

Expert guidance on selecting, implementing, and optimizing lab informatics systems.

Frequently Asked Questions

Common questions about choosing between ELN, LIMS, and LIS systems.

Do I need all three systems?

Most labs do not need all three. Research and pharma labs typically use an ELN paired with a LIMS. Clinical and diagnostic labs rely primarily on a LIS, sometimes with a LIMS for complex workflows. Only large academic medical centers with both research and clinical operations commonly deploy all three systems. Start with the system that addresses your most critical pain point and expand from there.

Can one system replace all three?

No single system fully replaces all three. Some vendors offer combined LIMS/LIS platforms or ELN modules within a LIMS, but these are typically strong in one area and limited in others. The core focus of each system — experiments (ELN), samples (LIMS), and patients (LIS) — requires fundamentally different data models, workflows, and regulatory considerations. Hybrid solutions can work for smaller labs with simpler needs, but most mid-to-large labs benefit from best-of-breed systems that integrate well.

How do these systems integrate with each other?

ELN, LIMS, and LIS systems integrate through APIs, HL7/FHIR interfaces, and middleware platforms. Common integration patterns include ELN-to-LIMS for pushing experimental results into sample records, LIMS-to-LIS for transferring analytical data to clinical workflows, and LIS-to-EMR for reporting patient results. Modern cloud-based systems typically offer better integration capabilities. The key is planning integration architecture before selecting individual systems, not after.

Which system should I implement first?

Start with the system that addresses your most critical operational bottleneck. Clinical labs processing patient specimens should prioritize a LIS for result reporting and regulatory compliance. Research labs struggling with sample tracking should start with a LIMS. Labs with IP documentation concerns should consider an ELN first. Phased rollouts reduce risk and help manage organizational change. Most implementations take 6-18 months depending on complexity.

What about SDMS and CDS — are those different too?

Yes, they serve different purposes. A Scientific Data Management System (SDMS) focuses on storing and organizing raw instrument data files like chromatograms, spectra, and images. A Chromatography Data System (CDS) is specialized for managing chromatographic instrument runs, data acquisition, and peak analysis. Both are complementary to ELN, LIMS, and LIS — not replacements. An SDMS often integrates with a LIMS to link raw data files to sample records, while a CDS feeds results into either a LIMS or ELN.

How much does each system typically cost?

Costs vary widely based on deployment model, user count, and complexity. Cloud-based ELNs start around $150-300 per user per month for basic plans. LIMS implementations range from $50,000 for small labs with SaaS solutions to $500,000+ for enterprise on-premise deployments including customization and validation. LIS systems for clinical labs typically cost $100,000 to over $1 million depending on scale, integrations, and regulatory requirements. Managed services models can significantly reduce upfront capital expenditure by spreading costs over monthly service agreements.

Not Sure Which Systems Your Lab Needs?

Our lab informatics experts can assess your workflows, regulatory requirements, and growth plans to recommend the right combination of ELN, LIMS, and LIS for your organization.