Nineteen map turtles (Graptemys spp.) maintained under natural conditions were investigated because of chronic shell abnormalities. Animals were evaluated using a novel shell scoring system that divided the 54 scutes into six regions, with each region scored for lesion extent and severity, and summated to produce a total shell disease score (TSDS). Complete blood counts and various biochemistry analytes (total protein, albumin, globulin, urea, uric acid, 25-hydroxycholecalciferol, phosphorus, and ionized and total calcium) were measured. Under ketamine-medetomidine-morphine anesthesia, cytology tape strips and full thickness shell biopsies were collected aseptically for microbiologic, histologic (including scoring of biopsy quality), and ultrastructural evaluations. The TSDSs were low and ranged from 4 to 22 (median=9) out of a possible score of 54. There were no correlations between TSDS and any hematologic or biochemistry parameter. The histologic quality of shell biopsies was good, and normal shell structure, by both light and electron microscopy, is described. Small clefts and pitting lesions were noted in 8/19 sections. There was no evidence of erosion, ulceration, inflammation, or infectious agents, but algae and diatoms were observed. Six biopsies yielded aerobic isolates (Chryseobacterium indologenes, Aeromonas hydrophila, Ralstonia pickettii, and Morganella morganii), whereas 11 shell samples grew various clostridial anerobes. No fungal organisms were cultured. Although the etiology of the lesions described remains unknown, the use of a scoring system in conjunction with full thickness biopsies is suggested to help standardize investigations into chelonian shell disease in the future.