This article presents an overview of the Finnish Prenatal Study of Autism and Autism Spectrum Disorders (FIPS-A), a new study designed to examine the relationship between prenatal serologic factors, mediating and moderating developmental antecedents, and risk of autism spectrum disorders (ASD). The FIPS-A is based on register linkages between births from 1987 to 2005 ascertained from the Finnish Medical Birth Register (FMBR) and other national registers on treatment for this group of disorders. All subjects were members of the Finnish Maternity Cohort (FMC), which consists of virtually all births in Finland from 1983 to the present, and which includes archived maternal serum samples. This study also capitalizes on other registry information, such as systematically collected data on pregnancy, prenatal and neonatal complications and manual data collection from well-child clinics providing developmental data from birth to the age of 7 years. In this paper, we describe the methods used in the FIPS-A study, including a description of the national registers, available data and case ascertainment procedures. Finally, we discuss implications of the data for future work on uncovering putative aetiologies of ASD and key strengths and limitations of the design.