Background: Factors leading to the wide range of manifestations associated with Mycoplasma pneumoniae (Mp) infection are unclear. We investigated whether Mp genotypes are associated with specific clinical outcomes. Methods: We compared Mp loads and genotypes of children with mucocutaneous disease to those with pneumonia, family members with upper respiratory tract infection (URTI), and carriers from a prospective cohort study (n=47; 2016–2017), and to other children with mucocutaneous disease from a case series (n=7; 2017–2020). Genotyping was performed using macrolide resistance determination, P1 subtyping, multilocus variable-number tandem-repeat analysis (MLVA), and multilocus sequence typing (MLST). Comparisons were performed with pairwise Wilcoxon rank sum test and Fisher exact test with corrections for multiple testing, as appropriate. Results:Mp loads did not statistically differ between patients with mucocutaneous disease and pneumonia or carriers. Macrolide resistance was detected in 1 (1.9%) patient with mucocutaneous disease. MLVA types from 2016–2017 included 3–5–6–2 (n=21, 46.7%), 3–6–6–2 (n=2, 4.4%), 4–5–7–2 (n=14, 31.1%), and 4–5–7–3 (n=8, 17.8%), and they correlated with P1 subtypes and MLST types. MLVA types were not associated with specific outcomes such as mucocutaneous disease, pneumonia, URTI, or carriage. They were almost identical within families, but varied over geographic location. MLVA types in patients with mucocutaneous disease differed between 2016–2017 (3–5–6–2, n=5, 62.5%) and 2017–2020 (4–5–7–2, n=5, 71.4%) (P=0.02). Conclusions: Our results suggest that Mp genotypes may not determine specific clinical outcomes.