Observations of the osteological features of malformations in lizards are currently limited. In examinations of ca. 1,300 Scincella specimens, one Scincella lateralis specimen and three S. boettgeri specimens were observed to have malformed digits, i.e., ectrodactyly. Each of these specimens had a malformation in only one limb. One S. lateralis specimen lacked digits I–III of manus, and three S. boettgeri specimens lacked digits I, II, or I and II of pedes. Micro-computed tomography scanning revealed that the phalanges and metacarpals of digits I–III were absent in the malformed S. lateralis specimen, whereas the malformed S. boettgeri specimens lacked all phalanges for externally absent toes but had five metatarsals, despite these being shorter in the absent toes than those in normal toes. Although malformed limbs have been reported previously in lizards, this is the first report based on osteological descriptions. Some genera of Scincidae include species that have undergone phylogenetic reduction of their digits. In such species, the developmental order of the phalanges and metacarpals/metatarsals is well-known from embryological studies. With reference to this developmental mechanism, we also discuss the assumed development of the malformed specimens observed in this study.