For full list of author affiliations and declarations see end of paper The present work aimed to evaluate the chromatin compaction of rooster spermatozoa along the male reproductive tract, and to study the vas deferens lining cells, potentially involved in sperm maturation. Chromomycin A3 (CMA3) was used to determine the chromatin compaction of spermatozoa from testis (T), proximal (including epididymis, V1), intermediate (V2) and distal (V3) vas deferens, and ejaculate (E). Six Birchen Leonesa roosters were used. E was obtained in vivo by dorso-ventral massage. V1, V2 and V3 sperm were obtained post mortem (six pairs of vasa deferentia), by flushing. T was obtained by washing the testes, cut in halves. The fixed cells were stained with CMA3 and propidium iodide for flow cytometry assessment. Results showed higher (P < 0.01) median fluorescence intensity (lower chromatin compaction) of T (693.8 ± 30.2) than V1 (546.3 ± 17.7), V2 (515.1 ± 12.1), V3 (517.6 ± 12.3) and E (491.4 ± 16.1). Regarding the percentage of intensely stained cells, T differs (P < 0.05) from V2, V3 and E, V1 differs (P < 0.05) from V3 and E, while V2, V3 and E do not differ. The histological analysis revealed secretory capacity of the vas deferens. Our findings specified that the transit though the vas deferens results in high percentage of compacted chromatin spermatozoa in E.