Quantifying testicular homogenization-resistant spermatid heads (HRSH) is a powerful indicator of spermatogenesis. These counts have traditionally been performed manually using a hemocytometer, but this method can be time consuming and biased. We aimed to develop a protocol to reduce debris for the application of automated counting, which would allow for efficient and unbiased quantification of rat HRSH. We developed a filter-lysis protocol that effectively removes debris from rat testicular homogenates. After filtering and lysing the homogenates, we found no statistical differences between manual (classic and filter-lysis) and automated (filter-lysis) counts using 1-way analysis of variance with Bonferroni's multiple comparison test. In addition, Pearson's correlation coefficients were calculated to compare the counting methods, and there was a strong correlation between the classic manual counts and the filter-lysis manual (r = 0.85, P = .002) and the filter-lysis automated (r = 0.89, P = .0005) counts. We also tested the utility of the automated method in a low-dose exposure model known to decrease HRSH. Adult Fischer 344 rats exposed to 0.33% 2,5-hexanedione in the drinking water for 12 weeks demonstrated decreased body (P = .02) and testes (P = .002) weights. In addition, there was a significant reduction in the number of HRSH per testis (P = .002) when compared to controls. A filterlysis protocol was optimized to purify rat testicular homogenates for automated HRSH counts. Automated counting systems yield unbiased data and can be applied to detect changes in the testis after low-dose toxicant exposure.