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Until recently, the LIMS and Laboratory Information System (LIS) have exhibited a few key differences, making them noticeably separate entities.

A LIMS traditionally has been designed to process and report data related to batches of samples from biology labs, water treatment facilities, drug trials, and other entities that handle complex batches of data. A LIS has been designed primarily for processing and reporting data related to individual patients in a clinical setting.

A LIMS may need to satisfy good manufacturing practice (GMP) and meet the reporting and audit needs of the regulatory bodies and research scientists in many different industries. A LIS, however, must satisfy the reporting and auditing needs of health service agencies e.g. the hospital accreditation agency, HIPAA in the US, or other clinical medical practitioners.

A LIMS is most competitive in group-centric settings (dealing with "batches" and "samples") that often deal with mostly anonymous research-specific laboratory data, whereas a LIS is usually most competitive in patient-centric settings (dealing with "subjects" and "specimens") and clinical labs. An LIS is regulated as a medical device by the FDA, and the companies that produce the software are therefore liable for defects. Due to this, an LIS can not be customized by the client.