The current century has been associated with the outbreaks of emerging and re-emerging viral infections with significant challenges for global public health. In this context, the occurrence of the recent three emerging viral infections, including SARS-CoV-2, MPXV, and ZIKV, have highlighted the potential of novel viral infections to affect societies all over the world (Ullah et al., 2023). Though commonly associated with respiratory and systemic presentations, the urogenital involvement has been increasingly reported as a potential sequelae linked to these viruses (Ullah et al., 2023; Creta et al., 2021; Gomez-Garberi et al., 2022). The urogenital system is composed of two distinct anatomical parts, including the urinary system (the kidneys, ureters, bladder, and urethra) and the genital system (the prostate, uterus, penis, testes, ovaries, and vagina) (Delaney et al., 2018; Tripathi et al., 2011; Schneider and Stein, 2009; Abolbashari et al., 2015; de Groat et al., 2009). Primarily as a respiratory viral infection, SARS-CoV-2 has been reported to be associated with urogenital complications such as acute kidney injury (AKI) and testicular impairment, and the recent MPXV outbreak was marked by urogenital involvement and sexual transmission (Gomez-Garberi et al., 2022; Zambrano et al., 2022; Chueh et al., 2020; La Marca et al., 2020). This system not only can be directly targeted by viral pathogens but also may act as a reservoir for viral persistence, which can facilitate long-lasting diseases and viral transmission (Kurscheidt et al., 2019a). For instance, the male genital tract, in particular, can be utilized as a potential immune-privileged anatomical site for some viral pathogens, such as ZIKV, promoting long-lasting viral persistence with significant consequences for sexual transmission (Kurscheidt et al., 2019a; Durant and Marzi, 2024). Despite the potential of these viruses to involve the urogenital system, a comprehensive analysis with a primary focus on the pathophysiological mechanisms underlying this involvement is lacking. The present review aims to provide a comprehensive review of urogenital manifestations of the recent three emerging viral infections, SARS-CoV-2, MPXV, and ZIKV, with a primary focus on describing their underlying pathophysiological mechanisms. It also addresses diagnostic considerations and therapeutic strategies in the context of urogenital sequelae associated with these viruses. Understanding the intricate molecular basis of these viral-caused sequelae is crucial for improving differential diagnosis and introducing targeted therapeutic strategies. To obtain relevant literature in this narrative review, a comprehensive search was done in PubMed, Scopus, and Web of Science databases, supplemented by cross-references from retrieved articles (studies from January 1995 and July 2025). The following keywords and Boolean operators were used in different combinations: “(SARS-CoV-2” OR “COVID-19”) AND (“urogenital system” OR “kidney” OR “testis” OR “fertility” OR “urinary tract”), (“Monkeypox” OR “MPXV” OR “mpox”) AND (“urogenital” OR “renal” OR “genital lesions”), (“Zika virus” OR “ZIKV”) AND (“urogenital system” OR “kidney” OR “testis” OR “semen” OR “fertility”). Performing this, original research articles, reviews, case reports, and meta-analyses discussing the urogenital manifestations, pathophysiological mechanisms, diagnostic aspects, or treatment considerations related to SARS-CoV-2, MPXV, or ZIKV were used. Screening was performed independently by two authors to ensure relevance (see Table 1).