The evolutionary origins of animal phyla are intimately linked with the Cambrian explosion, a period of radical ecological and evolutionary innovation that begins approximately 540 Mya and continues for some 20 million years, during which most major animal groups appear. Lophotrochozoa, a major group of protostome animals that includes molluscs, annelids and brachiopods, represent a significant component of the oldest known fossil records of biomineralised animals, as disclosed by the enigmatic ‘small shelly fossil’ faunas of the early Cambrian. Determining the affinities of these scleritome taxa is highly informative for examining Cambrian evolutionary patterns, since many are supposed stem-group Lophotrochozoa. The main focus of this thesis pertained to the stem-group of the Brachiopoda, a highly diverse and important clade of suspension feeding animals in the Palaeozoic era, which are still extant but with only with a fraction of past diversity. Major findings include adding support for tommotiid affinity as stem-group lophophorates. Determining morphological character homologies vital to reconstructing the brachiopod stem-group was achieved by comparing Cambrian Lagerstätten with the widespread biomineralised record of Cambrian stem-brachiopods and small shelly fossils. Polarising character changes associated with the putative transition from scleritome organisms to crown-group brachiopods was furthered by the description of an enigmatic agglutinated tubular lophophorate Yuganotheca elegans from the Chengjiang Lagerstätte, China, which possesses an unusual combination of phoronid, brachiopod and tommotiid characters. These efforts were furthered by the use of X-ray tomographic techniques that revealed novel anatomical features, including exceptionally preserved setae in the tommotiid Micrina. The evidence for a common origin of columnar brachiopod shell structures in the tommotiids is suggested and critically examined. Enigmatic and problematic early and middle Cambrian lophotrochozoans are newly described or re-described in light of new evidence, namely: the stem-brachiopod Mickwitzia occidens Walcott from the Indian Springs Lagerstätte, Nevada; a putative stem-group entoproct Cotyledion tylodes Luo and Hu from Chengjiang, China; a new enigmatic family of rhynchonelliform brachiopods exemplified by the newly described Tomteluva perturbata from the Stephen Formation, Canada; and the tommotiid Micrina etheridgei (Tate) from the Flinders Ranges, South Australia. Cladistic analyses of fossil morphological data supports a monophyletic Brachiopoda.