Purpose: Low skeletal muscle mass determined radiographically has emerged as an important prognostic marker in penile cancer patients but may be unrecognized in obese patients with a high comorbid disease burden. Moreover, publicly available software for image segmentation are limited. Thus, we describe the prevalence of radiographically low skeletal muscle mass in an obese penile cancer cohort, using an open-source software and examine its association with comorbid disease burden. Methods: This is a cross-sectional study, utilizing retrospective data from patients diagnosed with penile squamous cell carcinoma between October 2009 and December 2019. Available digital files of perioperative computerized tomography were analyzed, using CoreSlicer, an open-source image segmentation software. The correlation between radiographically low skeletal muscle mass, defined as a skeletal muscle index (SMI) less than 55 cm2/m2 and a Charlson Comorbidity Index (CCI) greater than 4 was examined, using logistic and linear regression. Results: Forty two of 59 patients had available digital files. Median SMI and body mass index (BMI) were 54.6cm2/m2 and 30.2kg/m2 respectively for the entire cohort. Of included patients, 54% had radiographically low skeletal muscle mass and a median BMI of 28.9 kg/m2. Radiographically low skeletal muscle mass was associated with a CCI greater than 4 on univariable and multivariable logistic regression with odds ratios of 4.85 (p = 0.041) and 7.32 (p = 0.033), respectively. When CCI was treated as a continuous variable on linear regression, the association between radiographically low skeletal muscle mass and CCI was positive, but not statistically significant with an estimated effect of 1.29 (p = 0.1) and 1.27 (p = 0.152) on univariable and multivariable analysis, respectively. Conclusion: Our data demonstrate that low skeletal muscle mass can be readily assessed with CoreSlicer and is associated with a CCI greater than 4 in obese penile cancer patients.