This research contributes to a better understanding of the mycotoxin problem associated with two important spices in world trade;, chilli and pepper by a multidisciplinary approach including analytical chemistry, risk assessment, food chemistry and predictive mycology. More specifically, this work provides important insights in mycotoxin contamination of these spices and associated risks in Sri Lanka. Firstly, a simple extraction method based on the QuEChERS approach was developed and successfully validated for the simultaneous determination of multiple mycotoxins using an advanced chromatographic technique, LC-MS/MS. The method was applied on complex spices for quantitative screening of seventeen mycotoxins. In addition to the classical aflatoxins and ochratoxin A, the spices were also found to be contaminated with several other toxicologically significant mycotoxins. Chilli samples (87%) were more frequently contaminated with mycotoxins than peppers (65%). Subsequently, the mycotoxins screening results and the collected consumption data were integrated in a quantitative risk assessment study. The results showed that AFB1 exposure via chilli consumption is of a public health concern in Sri Lanka, pepper is of lesser extent a risk due to the lower consumption. The toxigenic mould characterization in black peppers showed that Aspergillus flavus and/or Aspergillus parasiticus were the predominant moulds (73%) found, with considerable contamination (60%) of Penicillium spp. and A. niger. Furthermore, predictive mould growth models on peppercorns were developed at three temperatures and seven water activity levels for both A. flavus and A. parasiticus isolates. Based on the research, suitable storage conditions for black peppercorns were suggested and the way forward in managing the risk towards mycotoxins posed by the consumption of these two spices in Sri Lanka