Hydroxysteroid (17β) dehydrogenase type 3 (HSD17B3) is known to be the primary enzyme converting androstenedione (A) to testosterone (T) in human and mouse testes. It is therefore important for male development and reproductive health. Inherited HSD17B3 deficiency is a known cause of a disorder of sex development (DSD) in humans, where XY individuals are born with a female appearance due to testosterone deficiency, but are virilized during puberty as T starts to suddenly rise. Due to the rarity of the condition, many open questions remain on e.g. the compensatory source of testosterone, and the wider consequences of the T deficiency. We have established and characterized mouse lines lacking either HSD17B3 (3-KO), HSD17B1, or both (DKO). 3-KO males were born apparently phenotypically normal, but presented signs of undermasculinization at later ages, including delayed puberty, a shortened anogenital distance, subfertility with normal spermatogenesis, Leydig cell maturation defects, and lower size of many androgen-sensitive tissues. The cause of the undermasculinization was a fetal delay in testosterone production, but by birth and in adulthood 3-KO males produced significant amounts of testosterone due to massive upregulation of androstenedione production, and compensatory enzymes. In the DKO mice the fetal testosterone production was abolished almost completely, confirming HSD17B1 as the enzyme compensating for the lack of HSD17B3 in early development. The resulting undermasculinization in DKO was also much more drastic than in 3-KO. However, adult DKO testosterone production was comparable to 3-KO, indicating that yet other enzymes take over the compensation after puberty. In 3-KO, we also identified a novel developmental programming mechanism, where fetal androgen deficiency led to reduced kidney size in adult males. This mechanism resembles the effects of the so-called masculinization programming window, thus far only identified for reproductive organs. Finally, we observed that the lack of HSD17B3 led to weight gain through excess adipocity in male mice. Together, these results confirm that HSD17B3 is essential for properly functioning testosterone biosynthesis, but compensatory mechanisms exist, and that fetal androgen deficiency has long-lasting effects on later phenotype.