Systemic sclerosis (SSc) is characterized by a wide variety of symptoms and disease manifestations including joint pain, gastrointestinal dysfunction, interstitial lung disease, and cardiomyopathy. Using the Scleroderma Health Assessment Questionnaire (SHAQ) and Short Form-36 (SF-36) we explored how patient-reported physical health, mental health, and functional status related to these clinical characteristics and to cytokine levels utilizing the Hospital for Special Surgery Scleroderma Registry. In a cross-sectional study of 185 patients meeting the 2013 ACR/EULAR criteria for SSc, we compared disease features and patient-reported outcomes (PROs). Interleukin-6 (IL-6), interleukin-1β (IL1β), and tumor necrosis factor-α (TNFα) levels were assessed by luminex and ELISA assays in a subset of 32 patients. The Pearson correlation coefficient, Spearman correlation coefficient, two-sample t test or Wilcoxon rank sum test, ANOVA or Kuskal-Wallis test, and Pearson chi-squared or Fisher's exact test were performed as applicable to detect the association between disease manifestations, PROs, and blood biomarkers. The modified Rodnan skin score (MRSS) was positively correlated with SHAQ scores. Patients who had musculoskeletal involvement scored worse on both the SHAQ and SF-36. Lower levels of TNFα expression in PBMCs were also correlated with musculoskeletal involvement. No other significant correlations were found between clinical factors, PROs, and cytokine data. Musculoskeletal outcomes are a major determinant of quality of life and function in patients with SSc. These results emphasize the importance of musculoskeletal outcomes in clinical studies of SSc.