Paecilomyces variotti (P. variotti) is a fungal species found in soil, wood and some foods, and has been associated with some severe systemic infections. P. variotti has not been previously identified in carious tissue, and the aim of the present study is to report the presence of P. variotti in a deep carious lesion discussing its possible local and systemic associations. A 28 year-old male was submitted to extraction of the upper left second premolar (tooth #25) presenting a deep carious lesion. After extraction the tooth was cleaved in its long axis, and the infected dentinal tissue was curetted and submitted to microbiological analysis using CHROMagar® Candida medium and Malt Extract Agar. Macroscopic and microscopic analysis confirmed the presence of P. variotti in the carious tissue. Post-operatory period was uneventful, healing of the dental socket was complete, and the patient remained well during the follow-up period. P. variotti, a fungus not considered saprophyte in the oral cavity, was encountered in a deep caries lesion, and its potential association with local and systemic infections should be considered.