The S-FCM uses flow cytometry technology to measure sperm concentrations. Semen samples from 104 men attending a male infertility clinic were used to evaluate the reproducibility of results and the carryover rate with the S-FCM by performing between- and within-run imprecision analyses. In addition, sperm concentrations measured with the S-FCM were compared with those obtained by manual analyses with the Makler chamber and the improved Neubauer hemacytometer. The results showed that automated analyses with the S-FCM were highly reproducible and the carryover rate was 0.17% or less. In within-run imprecision assays, the coefficients of variation for the S-FCM were less than 5% at all sperm concentrations, while those for the Makler chamber were between 17.7% and 28.7% at lower sperm concentrations. The overall correlation between values measured with the S-FCM and those measured with the Makler chamber and improved Neubauer hemacytometer was excellent, but at lower sperm concentrations the correlation was lower. The S-FCM performed sperm concentration analyses in 110 seconds compared with 5 minutes for the Makler chamber and 10 minutes for the improved Neubauer hemacytometer. The S-FCM is suitable for quantitative measurement of lower sperm concentrations.