Coccidia are common endoparasites in reptiles, especially lizards. Within this class Choleoeimeria spp. infections are rarely detected, but they may have a high pathogenic potential and treatments are often unsuccessful. A retrospective study was performed evaluating the prevalence of Choleoeimeria in fecal samples from lizards submitted for routine examination to a diagnostic laboratory in Germany. Between 2013 and 2014, 1.5% (n = 24/1,621; 95% confidence interval [CI]: 1.0–2.2%) of coprological samples from different lizard species tested positive for Choleoeimeria oocysts using a fecal flotation technique. This prevalence was similar to data obtained 10 yr earlier at the same laboratory. Infected species included central bearded dragons (Pogona vitticeps), collared lizards (Crotaphytus collaris), unclassified agamids, monitors, one horned tree lizard (Acanthosaura sp.), one gecko, one common bluetongue (Tiliqua scincoides), and one chameleon. Different treatments (toltrazuril in varying intervals or trimethoprim and sulfonamide) in combination with strict environmental hygiene and disinfection with p-Chlor-m-Kresol did not impact fecal oocyst shedding for one juvenile Lawson's dragon (Pogona henrylawsoni). A new therapy approach using 10 mg/kg toltrazuril PO q 24 h for 3 days, with a repeat in 7 days, combined with 5 mg/kg clindamycin PO q 24 h for 7 days, finally resulted in negative oocyst shedding. Possible explanations for the challenging treatment of Choleoeimeria spp. are their localization in the gallbladder or the phylogenetical distance of the genus Choleoeimeria to the typical members of the family Eimeriidae. Further research is needed to increase our knowledge of these parasites and to develop an evidence-based treatment approach for diseased reptiles.