A number of disease-associated PrP forms characterized by abnormally short proteinase K–resistant fragments (atypical PrPres) were recently described in prion diseases. The relationship between atypical PrPres and PrPSc, and their role in etiology of prion diseases, remains unknown. We examined the relationship between PrPSc and atypical PrPres, a form characterized by short C-terminal proteinase K–resistant fragments, in a prion strain of synthetic origin. We found that the two forms exhibit distinct neuronal tropism, deposition patterns, and degree of pathological lesions. Immunostaining of brain regions demonstrated a partial overlap in anatomic involvement of the two forms and revealed the sites of their selective deposition. The experiments on amplification in vitro suggested that distinct neuronal tropism is attributed to differences in replication requirements, such as preferences for different cellular cofactors and PrPC glycoforms. Remarkably, deposition of atypical PrPres alone was not associated with notable pathological lesions, suggesting that it was not neurotoxic, but yet transmissible. Unlike PrPSc, atypical PrPres did not show significant perineuronal, vascular, or perivascular immunoreactivity. However, both forms showed substantial synaptic immunoreactivity. Considering that atypical PrPres is not associated with substantial lesions, this result suggests that not all synaptic disease–related PrP states are neurotoxic. The current work provides important new insight into our understanding of the structure–pathogenicity relationships of transmissible PrP states.