BACKGROUND: There are multiple adverse effects of anemia on human function, particularly on women. However, few researches are conducted on women anemia in rural Western China. This study mainly aims to investigate the levels and associated factors of maternal anemia between 2001 and 2005 in this region. METHODS: 6172 and 5372 mothers with children under three years old were selected from 8 provinces in 2001 and from 9 provinces in 2005 respectively in Western China by means of a multi-stage probability proportion to size sampling method (PPS). The blood samples were tested and related socio-demographic information was obtained through questionnaires. A two-level logistic regression model was employed to identify the determinants and provincial variations of women anemia in 2001 and 2005. RESULTS: The results indicated that the crude prevalence of women anemia in 2005 was higher than the rate in 2001(45.7% vs 33.6%). Based on the nationwide census data in 2000, the age-standardized prevalence of women anemia in the study were obtained as 38.0% in 2001 and 50.0% in 2005 respectively. Two-level logistic model analysis showed that compared to the average, women were more likely to be anemic in Guangxi and Qinghai in 2001 as well as in Chongqing and Qinghai in 2005; that women from Minority groups had higher odds of anemia in contrast with Han; that women with higher parity, longer breastfeeding duration and higher socioeconomic level had a lower rate of anemia, while age of women was positively associated with anemia. The positive correlation between women anemia and altitude was also observed. CONCLUSIONS: The study demonstrated that the burden of maternal anemia in rural Western China increased considerably between 2001 and 2005. The Chinese government should conduct integrated interventions on anemia of mothers in this region.