Compound Specific Isotope Analysis (CSIA) has been shown to be a useful tool for assessing biodegradation, volatilization, and hydrocarbon degradation. One major advantage of this technique is that it does not rely on determining absolute or relative abundances of individual components of a hydrocarbon mixture which may change considerably during weathering processes. However, attempts to use isotopic values for linking sources to spilled or otherwise unknown hydrocarbons have been hampered by the lack of a robust and rigorous statistical method for testing the hypothesis that two samples are or are not the same. Univariate tests are prone to Type I and Type II error, and current means of correcting error make hypothesis testing of CSIA source-apportionment data problematic. Multivariate statistical tests are more appropriate for use in CSIA data. However, many multivariate statistical tests require high numbers of replicate measurements. Due to the high precision of IRMS instruments and the high cost of CSIA analysis, it is impractical, and often unnecessary, to perform many replicate analyses. In this paper, a method is presented whereby triplicate CSIA information can be projected in a simplified data-space, enabling multivariate analysis of variance (MANOVA) and highly precise testing of hypotheses between unknowns and putative sources. The method relies on performing pairwise principal components analysis (PCA),then performing a MANOVA upon the principal component variables (for instance, three, using triplicate analyses) which capture most of the variability in the original data set. A probability value is obtained allowing the investigator to state whether there is a statistical difference between two individual samples. A protocol is also presented whereby results of the coupled pairwise PCA-MANOVA analysis are used to down-select putative sources for other analysis of variance methods (i.e., PCA on a subset of the original data) and hierarchical clustering to look for relationships among samples which are not significantly different. A Monte Carlo simulation of a 10 variable data set; tanks used to store, distribute, and offload fuels from Navy vessels; and a series of spilled oil samples and local tug boats from Norfolk, VA (U.S.A.) were subjected to CSIA and the statistical analyses described in this manuscript, and the results are presented. The analysis techniques described herein combined with traditional forensic analyses provide a collection of tools suitable for source-apportionment of hydrocarbons and any organic compound amenable to GC-combustion-IRMS.