Objective: To simultaneously detect fetal aneuploidies and single gene diseases using a novel noninvasive prenatal testing (NIPT) method called the Targeted And Genome-wide simultaneous sequencing (TAGs-seq). Design: Comparison of TAGs-seq NIPT results with conventional NIPT and diagnostic results. Setting: Shenzhen People’s Hospital and Chinese PLA General Hospital Population or Sample: 26 normal pregnancies, 7 pregnancies with fetal aneuploidies, 7 pregnancies with fetal achondroplasia (ACH) or thanatophoric dysplasia (TD), 18 pregnancies with ACH/TD-like ultrasound findings, and 10 pregnancies with fetal risk of beta-thalassemia. Methods: Plasma cfDNA was amplified by TAGs-seq to simultaneously obtain the whole-genome sequence of 0.1-3× depth and reads on target genes of >1000× depth. The whole-genome sequence was analyzed for fetal aneuploidy risk using a binary hypothesis T-score, and the reads on target genes were analyzed for single gene diseases by calculating minor allelic frequency of loci on FGFR3 and HBB. Main Outcome Measures: Concordance between the TAGs-seq NIPT, conventional NIPT and diagnostic results. Results: Consistent to conventional NIPT and diagnostic results, all cases of fetal aneuploidies and fetal ACH/TD were correctly identified from 58 pregnancies by TAGs-seq NIPT with high sensitivities and specificities. Two cases of paternal mutations of beta-thalassemia were correctly identified by TAGs-seq NIPT from 10 pregnancies, although one false-negative result was obtained. Conclusions: The TAGs-seq assay demonstrated a good potential to simultaneously detect fetal aneuploidies and single gene diseases as a novel NIPT method.