Infertility becomes a global problem that affects to the same extent females and males. As reasons of male infertility can differ among individuals, the accurate diagnostics is essential for effective treatment. The most problematic both in diagnostics and in treatment are disturbances of spermatogenesis. Seminal fluid is rich in proteins that potentially can serve as markers for male infertility and among them, markers of spermatogenesis which are highly desired. To find biomarkers of spermatogenesis, we applied comparative proteomics using nano ultra performance liquid chromatography and tandem mass spectrometry (nanoUPLC-MS/MS) followed by single-sample Western blotting (WB) using seminal fluid samples from males with different types of infertility including non-obstructive azoospermia (NOA), cryptozoospermia (C) and severe oligozoospermia (SO). Then, the extensive survey on the identified proteins and their function in male reproductive system has been done. The proteomic approach has enabled to identified five seminal fluid proteins being potential markers of spermatogenesis disorders: ADGRG2, RAB3B, LTF, SLC2A3 and spermine synthase (SMS). Among them ADGRG2 seems to be strongly involved in male infertility. In addition, WB indicated that the distribution of LTF, SLC2A3 and SMS was not coherent among the individuals, especially in a group with NOA. Functional annotation analysis and search in proteomics databases revealed that vast majority of the proteins originated from extracellular environment. The presented data point out several proteins that potentially can become biomarkers of male infertility. The data suggest, however, different mechanisms behind the male infertility indicating that the etiology is more complex. We assume that recognition of these mechanisms may lead to the creation of specific protein panel helpful in the management of male infertility and therefore, further studies are required.