Molecular methodologies while highly advantageous do contain limitations and certain disadvantages. These can include:

Cost: Molecular methodologies are usually more expensive than standard traditional methodologies. Equipment and reagent costs could be prohibitive to some laboratories. As molecular methods become more standard, the costs could potentially decrease. Currently, laboratories that consider the cost prohibitive prefer to transport molecular specimens to a reference laboratory.

Personnel requirements: Depending on laboratory accreditation requirements and testing methodologies some personnel may not be qualified to competently perform molecular testing.

Laboratory space requirements: Molecular amplification methods require dedicated space that may not be available in some clinical laboratories.