In many plant species, prolonged application of ammonium (NH4+) as a source of nitrogen results in physiological and morphological disorders (‘ammonium toxicity’). In the mustard (Sinapis alba L.) seedling we have previously observed particularly severe symptoms of ammonium toxicity in the absence of external nitrate (NO3‐) or with increasing NH4+/NO3‐ ratios. In the present investigation we have studied the symptoms of this ‘toxicity’in more depth, i.e. at the morphological, plastidic, enzyme and mRNA levels, in an effort to elucidate the causation of the syndrome.It could be confirmed that the syndrome is specific for ammonium and is not caused by a surplus of nitrogen. The syndrome is caused neither by pH changes in the medium nor by non‐specific osmotic effects. Furthermore, the syndrome is not causally related to the fact that nitrate reductase (NR; EC 1.6.6.1.) is induced by ammonium. Development of the syndrome requires neither photosynthesis nor intact plastids. Nevertheless, the plastids are severely affected by ammonium application as is anthocyanin synthesis.Enzymes are differently affected. Among the plastidic enzymes, levels of ribulose‐1,5‐bisphosphate carboxylase (RuBPCase; EC 4.1.1.39) and NADP‐dependent glyceraldehyde‐3‐phosphate dehydrogenase (NADP‐GPD; EC 1.2.1.13) are strongly reduced and abundance of translatable mRNA of the small subunit of RuBPCase is decreased, whereas nitrite reductase (NIR; EC 1.7.7.1) is not affected. Among extraplastidic enzymes, the level of chalcone synthase (CHS; EC 2.3.1.74) is strongly reduced, the NAD‐dependent glyceraldehyde‐3‐phosphate dehydrogenase (NADGPD; EC 1.2.1.12) level is unaffected, whereas the isocitrate lyase (ICL; EC 4.1.3.1) level is strongly promoted.The fat → carbohydrate transformation seems to be impaired by ammonium: fat degradation is reduced, starch accumulation is strongly inhibited and the levels of glucose and fructose are decreased.It appears from the present data and from results obtained in a companion study (U. Hecht and H. Mohr, in preparation) that the ammonium toxicity syndrome is detectable as soon as ammonium accumulation occurs in the plant. However, the actual mechanism through which the excess ammonium affects metabolism remains unclear at present.