Animal models of tinnitus rely on interpretation of behavioural or reflexive tests to determine the presence of this phantom perception. A commonly used test is the gap prepulse inhibition of acoustic startle (GPIAS), which is often combined with prepulse inhibition (PPI) to ensure that reduced GPIAS suppression is not due to hearing loss caused by the acoustic trauma commonly used to trigger tinnitus development. In our laboratory GPIAS and PPI are routinely used on two colonies of outbred tri-colour guinea pigs. However, our results show that these colonies show divergent results even before any tinnitus-inducing treatment, which impacts their suitability in tinnitus models. Although colony 1 and 2 show similar results in PPI (~95% of animals showing significant suppression), only ~30% of colony 2 also shows significant suppression in GPIAS compared to ~75% of colony 1. Cochlear sensitivity measured using compound action potentials showed no significant differences between colonies. Therefore, peripheral threshold loss was excluded as a possible factor. Our results show that similar strains of laboratory animals can show highly divergent results and GPIAS testing for tinnitus will not work for every animal strain. In addition, our data support the notion that PPI and GPIAS responses may rely on different neural circuitry.