Marx's vast reference files, which consist mainly of newspaper and magazine clippings, represent the second largest series in the collection. These include three subseries of topical reference files arranged alphabetically within three broad chronological groupings. The topics in these files cover reproductive health and technology, Roman Catholic moral teaching and Church-related controversies, and a variety of human life issues. The largest topics are abortion, AIDS, contraception, euthanasia, and sex education programs, the primary foci of Marx's mission as the founder and longtime director of HLI. Based upon the date of the materials enclosed in each grouping, Marx appears to have restarted the otherwise fairly congruent sets of reference files once in 1975 and again around 1978. There is considerable chronological overlap between materials in each of these subseries, as noted in the subseries titles. The first of these three subseries mostly includes materials dating from 1960, while some items, chiefly sermons and sermon notes which Marx wrote as a young priest, stretch the collection back to 1947. (n.b.: The sermons, which might fit more appropriately with the writings and course materials, remain where Marx himself kept them filed.)

Following the reference files comes a set of files kept on various organizations and a short collection of articles written by other individuals, many of which appeared in HLI publications. Both are arranged alphabetically, the first by the organizations' names and the second by the authors' last names. The organization files typically contain literature produced by the organizations themselves, but may also hold relevant newspaper clippings and some correspondence.