Approximately 50% of publications in English peer reviewed journals are contributed by non-native speakers (NNS) of the language. Basic thought processes are considered to be universal yet there are differences in thought patterns and particularly in discourse management of writers with different linguistic and cultural backgrounds. The study highlights some areas of potential incompatibility in native and NNS processing of English scientific papers. Principles and conventions in generating academic discourse are considered in terms of frequently occurring failures of NNS to meet expectations of editors, reviewers, and readers. Major problem areas concern organization and flow of information, principles of cohesion and clarity, cultural constraints, especially those of politeness and negotiability of ideas, and the complicated area of English modality pragmatics. The aim of the paper is to sensitize NN authors of English academic reports to problem areas of discourse processing which are stumbling blocks, often affecting acceptance of manuscripts. The problems discussed are essential for acquiring pragmalinguistic and sociocultural competence in producing effective communication.