Mitral valve prolapse has generally been associated in adults with a thin body habitus. However, prior studies used biased samples or limited anthropometric measures. In addition, no information has been available on the subjective assessment of body habitus and diagnosis of mitral valve prolapse, especially in children. We conducted a cross-sectional study on 813 children with uniform assessment of anthropometric measures and mitral valve prolapse. Consistent with research conducted on adults, those subjects with mitral valve prolapse were lighter, thinner, and had, on average, lower values for several, quantifiable anthropometric parameters with the exception of height. However, the subjective assessment showed that while the assessment did not differ by diagnosis, those subjects with mitral valve prolapse were never described as fat. These data support an association between mitral valve prolapse and slender body habitus and extends it to children, thus underscoring the clinical importance that a thin body habitus may be a marker for mitral valve prolapse throughout the age span. This association may partly explain the observed genetic distribution of mitral valve prolapse.