Human reproductive system involve a number of intricate complex interconnected physiological metabolic pathways and metabolites with involvement of overall health of different body organs. Overall health alterations mediated physiological conditions such as obesity, diabetes etc. bring about additional variations in expression and presence of metabolic constituents including kinases, hormones, proteins, peptides. The detailed analysis of various molecules like endocrine hormones, neuropeptides, immunity and inflammation associated kinases and proteins that have an end effect in cells and tissues, and might be playing a role in impacting male reproduction have been deliberated here. A deliberative collection of obesity and infertility related molecules including endocrine hormones, cytokines, adipokines, adiponectin, resistin, visfatin, ghrelin, orexins, leptin, adropin, chemerin, along with diabetes and age related physiological impact analysis on male reproductive system have been included in this selective compilation. An in-depth understanding of changes and introduction of new intermediate molecules for regulation of physiological phenomena like energy homeostasis in obesity regulation and their interlinked associated impact on the male fertility potential would provide a reflection for possible development of new therapeutics.