In the last decade compound-specific stable isotope analysis (CSIA) has evolved as a valuable technique in the field of environmental science, especially in contaminated site assessment. Instrumentation and methods exist for highly precise measurements of the isotopic composition of organic contaminants even in a very low concentration range. Nevertheless, the determination of precise and accurate isotope data of environmental samples can be a challenge. Since CSIA is gaining more and more popularity in the assessment of in situ biodegradation of organic contaminants, an increasing number of authorities and environmental consulting offices are interested in the application of the method for contaminated site remediation. Because of this, it is important to demonstrate the problems and limitations associated with compound-specific isotope measurements of environmental samples. In this review, potential pitfalls of the analytical procedure are critically discussed and strategies to avoid possible sources of error are provided. In order to maintain the analytical quality and to ensure the basis for reliable stable isotope data, recommendations on groundwater sampling, and sample preservation and storage are given. Important aspects of sample preparation and preconcentration techniques to improve sensitivity are highlighted. Problems related to chromatographic resolution and matrix interference are discussed that have to be considered in order to achieve accurate gas chromatography/isotope ratio mass spectrometry measurements. As a result, the need for a thorough investigation of compound-specific isotope fractionation effects introduced by any step of the overall analytical method by standards with known isotopic composition is emphasized. Finally, we address some important points that have to be considered when interpreting data from field investigations. [Figure not available: see fulltext.] © 2007 Springer-Verlag.