Background: While cigarette smoking is a well-established risk factor for bladder cancer (BC), limited research has explored the contribution of waterpipe smoking (WPS) to BC. WPS is gaining popularity among Middle Eastern youth, often perceived as a safer alternative to cigarettes. Alarmingly, Lebanese males had an age-standardized incidence rate of 54.0 per 100,000 in 2019, the highest in the Arab World and five times the global average, prompting a critical investigation into potential risk factors. Mounting evidence suggests that WPS exposes users to toxicants and carcinogens that can induce chromosomal damage contributing to cancer. This study aims to assess the genomic and mutational profiles of BC in waterpipe smokers compared to cigarette smokers. Methods: This cross-sectional study enrolled adults with urothelial carcinoma (UC) who exclusively smoked waterpipe at the American University of Beirut Medical Center (AUBMC) between April 2017 and September 2019. Next-generation sequencing by MSK-IMPACT characterized mutational profiles, tumor mutation burden, and microsatellite instability (MSI) status in tumor-normal pairs. For comparison, a cohort from Memorial Sloan Kettering Cancer Center (MSKCC), comprising previously profiled BC tumors from cigarette smokers, was used. Results: A total of 14 exclusively WPS-BC patients were enrolled, with 12 males (85.7%) and a median age at diagnosis of 62.9 years (range: 30.7 to 78.9). Among these patients, 9 (64.3%) had non-muscle invasive BC, with 8 (57.2%) classified as high-grade UC. MSK-IMPACT sequencing successfully analyzed 13 WPS samples, revealing genomic patterns similar to the cigarette smoking cohort. Common genetic alterations in the WPS cohort included mutations in TERT promoter (62%), TP53 and FGFR3 (46% each), and PIK3CA (38%). Mutations in chromatin modifiers were less prevalent, with the highest frequencies observed in KDM6A (31%) and KMT2C (15%). The tumor mutation burden was higher in the WPS group (22 per MB) compared to the cigarette smoking cohort (9 per MB), with no definite evidence of MSI. PD-L1 expression was generally low, with only 2 samples exhibiting combined positivity scores (CPS) of 15 and 10, primarily associated with immune cells PD-L1 expression. Only one tumor demonstrated 3% PD-L1 expression on tumor cells, while 7 tumors displayed no expression on either tumor or immune cells (CPS of 0). Conclusions: This study underscores the genomic similarities between BC in waterpipe and cigarette smokers. The preliminary findings, limited by sample size, highlight the need for further investigations to elucidate the potential role of WPS in BC development. Future efforts will focus on cohort expansion to validate initial observations, raising awareness of health risks associated with WPS, and emphasizing the importance of continued research to inform preventive strategies.