The Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA) enables small-scale gel electrophoretic separation of nucleic acids on a microfluidic chip. Shortage of chips and excess reagents is a common issue. This report explored the compatibility of two commonly used Bioanalyzer reagents with three Bioanalyzer chip types. Microfluidic electrophoretic separation of DNA and RNA using DNA High Sensitivity and RNA 6000 Nano reagents, respectively, was successfully performed on multiple chip types, following the assay-specific protocol. For RNA quality and next-generation sequencing library size estimation, the Bioanalyzer chip s tested can be used interchangeably. These findings will be valuable for any laboratory using the Agilent Bioanalyzer in a shared facility.