<p>Background: Balanced translocation and azoospermia as two main reasons for recurrent pregnancy loss are known to be the leading causes of infertility across the world. Balanced translocations in azoospermic males are very rare and extensive studies need to be performed to elucidate the translocation status of the affected individuals. &nbsp;<br /> Case Presentaion: The cytogenetic characterization of a 28 year old male and his female partner is reported in this study. The male partner was diagnosed with non-obstructive azoospermia (NOA) and the couple was unable to conceive. Cytogenetic analysis by karyotyping through Giemsa-trypsin-giemsa banding technique (GTG) showed a novel balanced translocation, 46,XY,t(19;22)(19q13.4;22q11.2), 13ps+ in the male and the female karyotype was found to be 46,XX. Multicolor fluorescence in situ hybridization (mFISH) analysis on paternal chromosomal preparations confirmed both the region and origin of balanced translocation. The status of Y chromosome microdeletion (YMD) was analyzed and no notable microdeletion was observed. Furthermore, protein-protein interaction (PPI) network analysis was performed for breakpoint regions to explore the possible functional genetic associations.<br /> Conclusion: The azoospermic condition of the male patient along with novel balanced chromosomal translocation was responsible for infertility irrespective of its YMD status. Therefore, cytogenetic screening of azoospermic patients should be performed in addition to routine semen analysis to rule out or to confirm presence of any numerical or structural anomaly in the patient.</p>