“which”如果使用不当可引起歧义。它常与“that”混用。“that”和“which”都引导定语从句，但“that”用于引导限定性从句，而“which”用于引导非限定性从句。
例如，“the sections that were positive for GFP were subjected to cell counting procedures”，在这个句子中，“that”引导的是限定性从句明确规定了是哪些切片用于细胞计数。相比之下，“the sections, which were positive for GFP, were subjected to cell counting procedures”，在这个句子中，对用于细胞计数的切片的规定相当宽松，可能指的是前一个句子或相临句子中提及的切片。提及GFP阳性的从句可以向读者提供一些额外的信息，但对于理解该句子的意义来说并非必不可少；也就是说，它是可有可无的。考虑到“which”的这种角色，研究人员在撰写论文时应明确“which”一词确切指代的东西——有时指代的是该词所紧跟的事物(这是最常见的)，有时指代的则是该句子的主语。
例如，“microglia migrated to the site of the lesion, which was associated with increased levels of ED-1”，这个句子就写得含混不清，因为我们很难确定“which”所指的到底是lesion，还是migration of microglia。如果读者可能会对此类句子产生疑惑，最好是推翻重写；例如，可以改为“migration of microglia to the site of the lesion was associated with increased levels of ED-1”，也可改为“microglia migrated to the site of the lesion, and immunohistochemical analysis revealed increased levels of ED-1 at this site”。两者均无歧义。
•“Data were normalised to the housekeeping gene actin, which was used as an internal reference…” (在这个句子中,“which”指代的是actin，因此actin也就是该从句的主语)
•“Data were normalised to the internal reference housekeeping gene actin, revealing increases in the levels of…”(如指随后从句中的分析数据,使用“which revealed”是不恰当的，且会造成歧义)
