Introduction Nowadays, an important decision for pregnant women is whether to undergo prenatal testing for aneuploidies and which tests to uptake. We investigate the factors influencing women's choices between non-invasive prenatal testing (NIPT) and invasive prenatal tests in pregnancies with elevated a priori risk of fetal aneuploidies. Methodology This is a mixed-method study. We used medical data (1st Jan 2015-31st Dec 2015) about women participating in further testing at Fetomaternal Medical Center at Helsinki University Hospital and employed Chi-square tests and ANOVA to compare the groups of women choosing different methods. Multinomial logistic regressions revealed the significant clinical factors influencing women's choice. We explored the underlying values, beliefs, attitudes and other psychosocial factors that affect women's choice by interviewing women with the Theory of Planned Behavior framework. The semi-structured interview data were processed by thematic analysis. Results Statistical data indicated that gestational age and counseling day were strong factors influencing women's choice. Interview data revealed that women's values and moral principles on pregnancy and childbirth chiefly determined the choices. Behavioral beliefs (e.g. safety and accuracy) and perceived choice control (e.g. easiness, rapidness and convenience) were also important and the major trade-offs happened between these constructs. Discussion Values are the determinants of women's choice. Service availability and convenience are strong factors. Medical risk status in this choice context is not highly influential. Choice AIDS can be developed by helping women to identify their leading values in prenatal testing and by providing lists of value-matching test options and attributes.