Poor sperm morphology and an elevated DNA fragmentation level are considered to be related to spermiogenesis malfunctions as a result of genetic mutations and effects of environmental factors, including industrial pollution. Standardized cross-sectional population studies of sperm morphology defects and sperm DNA fragmentation, especially in regions with increased environmental pollution may be helpful to investigate an influence of industrial pollution and other population-related factors on spermiogenesis process. The aim of present study was to estimate an influence industrial pollution on sperm morphogenesis and sperm DNA fragmentation in men from the general population of the Western Siberia. The Novosibirsk and Kemerovo cities are located to same climatic conditions in Western Siberia but the Kemerovo city is characterized by increased environmental pollution especially by particulate matter (PM). The male volunteers living in Novosibirsk (n = 278) and Kemerovo (n = 258) were enrolled. Percentages of sperm morphological defects are counted after staining native ejaculate smears by Diff-Quick kits. DNA fragmentation was estimated by a SCSA technique. The residents of Kemerovo were characterized by lowered sperm count and sperm motility, elevated DNA fragmentation, poor sperm morphology and increased incidence of morphological effects of head (pyriform, elongated, round, abnormal acrosome and vacuolated chromatine), asymmetrical neck insertion and excess residual cytoplasm. Moreover, elevated DNA fragmentation was associated with lowered sperm count, sperm motility and increased percentages of several sperm morphology defects, with the place of residence affecting the relationships between conventional semen parameters, sperm morphology and DNA fragmentations. Our study suggests that excessive sperm head elongation and impaired acrosome formation can contribute to sperm morphology deterioration in men from polluted areas. Regional features in the relationships between sperm morphology, sperm count and DNA fragmentation were shown, suggesting an importance of studying sperm morphology pattern in men from different regions.