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Osteoporosis is a multifactorial systemic skeletal disease that is characterized by a low bone mineral density (BMD) and the microarchitectural deterioration of bone tissue, leading to bone fragility. The search for new genes that may play an important role in the regulation of bone mass and the development of osteoporosis is ongoing. Recently, it was found that altering the activity of the endothelin-1-converting enzyme encoded by the <i>ECE1</i> gene may affect bone mineral density (BMD). Another gene involved in the process of osteoblast differentiation and maturation is believed to be <i>PPARG</i> (peroxisome proliferator-activated receptor gamma). This participates in regulating the transformation of stem cells and affects the process of bone formation and resorption. Therefore, we analyzed the association of the <i>ECE1</i> and <i>PPARG</i> variants with osteopenia and osteoporosis risk in the Polish population. This study included a group (<i>n</i> = 608) of unrelated Polish women (245 individuals with osteoporosis (aged: 57 ± 9), 109 individuals with osteopenia (aged: 53 ± 8) and 254 healthy controls (aged: 54 ± 8)). The real-time PCR technique was used to determine the genetic variants for rs213045 (-338<i>G</i>><i>T</i>) and rs213046 (-839<i>A</i>><i>C</i>) of the <i>ECE1</i> gene and rs1801282 (Pro12Ala, <i>C</i>><i>G</i>) of the <i>PPARG</i> gene. Analysis of the <i>PPARG</i> rs1801282 variants did not show any association with the risk of osteoporosis and osteopenia. However, in the densitometric results, lower median Z-score values were observed for the <i>T</i> allele compared to the <i>G</i> allele for the rs213045 variant of the <i>ECE1</i> gene (−1.11 ± 1.07 vs. −0.78 ± 1.21, <i>p</i> = 0.021). Moreover, the <i>TT</i> genotype for the rs213045 variant was more common in women with osteopenia (13.8%, OR = 2.82, <i>p</i> < 0.05) and osteoporosis (7.8%, OR = 1.38, <i>p</i> > 0.05) compared to the control group (5.5%). Additionally, our results suggested that the T allele of rs213045 was more common in women with osteopenia compared to the controls. We further observed that the haplotype containing two major <i>GA</i> alleles of <i>ECE1</i> (rs213045, rs213046) could reduce the risk of osteopenia in our population. Finally, we found that women with osteoporosis had statistically significantly lower body mass and BMI values compared to the control group. Our results suggest that the <i>ECE1</i> rs213045 variant may increase the risk of osteopenia. However, the data obtained require confirmation in further studies.