The current stumpage price in harvesting of a 50-year-old sugi (Japanese cedar, Cryptomeria japonica) plantation is not enough to motivate forest owners to reforest. Therefore, it is vital to reduce the cost for reforestation after logging as well as for logging and wood transportation of the preceding stands. Low initial tree density has been emphasized as one of the important basic measures to reduce directly the reforestation costs. In this study, for better understanding of the mechanical properties and dimensional stability of lumbers from sugi trees grown in low initial tree density, we examined the effects of initial tree density on wood density and microfibril angle of the S2 layer in the secondary wall of tracheids in rings from pith to bark in a sugi cultivar (Tosaaka) grown in a Nelder plot (initial density zoning symbols; D (4823 trees/ha), E (3349 trees/ha), G (1615 trees/ha), H (1122 trees/ha) and J (541 trees/ha)). Ring width and latewood percentage in J tree (541 trees/ha) were significantly larger and smaller than those of other initial tree density zoning symbol trees, respectively. Average wood density and earlywood wood density in J tree (541 trees/ha) were significantly smaller than those of other initial tree density zoning symbol trees (Tukey’s honestly significant difference test (Tukey HSD), p < 0.05). However, effects of initial tree density on the microfibril angles (earlywood and latewood) in rings from pith to bark and the transition patterns of microfibril angle from earlywood to latewood in an outer ring (ring number 22) were not significant or very small. Heartwood width in H trees (1122 trees/ha) and J trees (541 trees/ha) were significantly larger than those in other initial tree density zoning symbol trees (Tukey HSD, p < 0.05). There were no significant differences of ring width, average wood density, earlywood density and microfibril angle between H trees (1122 trees/ha) and E trees (3349 trees/ha) in many rings from pith to bark (Tukey HSD, p > 0.05). Based on these results of Tosaaka, a sugi cultivar grown in a Nelder plot, it was assumed that mechanical properties and dimensional stability of lumbers from sugi trees grown in low initial tree density (1000 trees/ha) might be quite similar to those from sugi trees grown in the regular initial tree density (3000 trees/ha), although lumbers from J trees (541 trees/ha) might be different from those of sugi trees grown in the regular initial tree density (3000 trees/ha). By taking the effects of genetic factor (variation of sugi cultivars) and the interaction between genetic and environmental factor (initial tree density) into consideration, the effects of low initial tree density (1000 trees/ha) on mechanical properties and dimensional stability of lumbers from sugi plantations in Japan might be smaller than the effects recognized in Tosaaka in this study. In this study, we did not examine the effects of initial tree density on the knots and the cross grain of lumbers. Low initial tree density might increase the negative effects of knots and cross grain on mechanical properties of lumbers. However, recent wood processing technology could minimize these negative effects.