Fine needle biopsy (FNB) with cytology has long been regarded as an excellent technique as the first choice for diagnosing adult tumours. Being an inexpensive minimally invasive technique with high accuracy and diagnostic immediacy through rapid on-site evaluation, it is also ideal for implementation in the paediatric setting, particularly in developing countries. Furthermore, it allows complementary and advanced procedures such as flow cytometry, polymerase chain reaction (PCR) or fluorescence in situ hybridization (FISH), among others, which enhances the diagnostic capacity of this technique and gives it a key role in risk stratification and therapeutic decision-making for several tumours. The advantages of FNB are optimized in the setting of a multidisciplinary team where cytologist, clinician and radiologist play leading roles. Paediatric tumours are rare and most ancillary techniques are cost-effective but complex to be implemented in small centres with limited experience in paediatric pathology. Therefore reference centres are essential, in order to establish teams with extensive experience and expertise. Hence, any child with a suspected malignancy should be directly referred to a paediatric oncology unit. Focusing on a practical approach to the assessment of paediatric lymphadenopathies and non-central nervous system solid tumours we review the effectiveness of FNB as applied concurrently with ancillary techniques in a multidisciplinary approach to the diagnosis, prognosis and therapeutic decisions of paediatric tumours and tumour-like lesions.