This study examined the effects of metabotropic glutamate receptor 6 (mGluR6) deficiency on ribbon synapse formation in rod spherules and cone pedicles using serial-section electron microscopy. In a wild-type (WT) mouse, only 3% of spherules had one invaginating bipolar dendrite (1B-type) and 97% of spherules were 2B-type. In contrast, in an mGluR6-knockout (KO) mouse, 29% of spherules were 1B-type and 71% of spherules were 2B-type. Spherules without bipolar invagination were not observed in either genotype. The single invaginating dendrites in 1B-type spherules were larger and the surface areas of synaptic ribbons were 23% smaller in the mGluR6-KO mouse than in the WT mouse. In cones, the number of invaginating bipolar dendrites decreased from 12 in the WT mouse to 9.5 in the mGluR6-KO mouse. This decrease correlated with a decrease in the number of cone synaptic ribbons from 10 in the WT mouse to 8 in the mGluR6-KO mouse. The mGluR6-KO phenotype showed negative effects on ribbon synapse formation. This negativity was similar to those in mGluR6-nob4, Gβ3-KO, Gβ5-KO, and RGS-7:RGS-11 double-KO mice, but the detailed manners and degrees of alterations appeared to vary depending on different missing components. Two published morphological assessments of the RGS-7:RGS-11 double-KO phenotype reported conflicting data; therefore, we tested the statistical techniques used in the two analyses. One statistical evaluation measure was effective in identifying a significant difference in structure between the mutant and WT phenotypes, whereas the other measure was ineffective. Conventional random section analysis using the effective measure provided sufficient data for a statistical test of the occurrence of structural changes. However, serial section analysis was required to determine the absolute numbers of ribbons and invaginating dendrites and to estimate structural parameters such as ribbon surface area.