The distinction between basic sciences and clinical knowledge which has led to a theoretical debate on how medical expertise is developed has implications for medical school and lifelong medical education. This longitudinal, population based observational study was conducted to test the fit of three theories--knowledge encapsulation, independent influence, distinct domains--of the development of medical expertise employing structural equation modelling. Data were collected from 548 physicians (292 men--53.3%; 256 women--46.7%; mean age = 24.2 years on admission) who had graduated from medical school 2009-2014. They included (1) Admissions data of undergraduate grade point average and Medical College Admission Test sub-test scores, (2) Course performance data from years 1, 2, and 3 of medical school, and (3) Performance on the NBME exams (i.e., Step 1, Step 2 CK, and Step 3). Statistical fit indices (Goodness of Fit Index--GFI; standardized root mean squared residual--SRMR; root mean squared error of approximation--RSMEA) and comparative fit (X[superscript 2][subscript D], X[superscript 2]) of three theories of cognitive development of medical expertise were used to assess model fit. There is support for the knowledge encapsulation three factor model of clinical competency (GFI = 0.973, SRMR = 0.043, RSMEA = 0.063) which had superior fit indices to both the independent influence and distinct domains theories (X[superscript 2][subscript 29] = 88.11 vs X[superscript 2][subscript 29] = 443.91 [X[superscript 2][subscript D] = 355.80] vs X[superscript 2][subscript 29] = 514.93 [X[superscript 2][subscript D] = 426.82], respectively). The findings support a theory where basic sciences and medical aptitude are direct, correlated influences on clinical competency that encapsulates basic knowledge.