The dataset provides detailed information on plant diseases, pests and estimates of the harmful effects of their spread in Lithuania. This package combines three closely related sources of information: a catalogue of plant pests, a catalogue of plant diseases and estimates of the harmful effects of observed harmful organisms for the analysis of the plant protection and agricultural sector. The pest catalogue includes data on the most common plant pests in Lithuania. Each pest is assigned a Lithuanian and Latin name, a group of biological dependency, a description, favourable spreading conditions and a limit of harmfulness. The package also sets out which plants are damaged by the pest, what are the main signs of damage and what control measures apply to their management. Each entry has been supplemented by recommendations on the management of resistance, specifying the means and conditions under which the spread of pests can be prevented most effectively. The catalogue of plant diseases shall contain information on plant diseases and their agents, the circumstances of their spread, favourable conditions and damage to plants. The record of each disease shall indicate which plant group it belongs to, a description of the disease, its symptoms and the species of vulnerable plants. The data contained in the package makes it possible to identify both isolated diseases and more complex pathological complexes that affect specific plants during different growing periods. At the same time, the recommended control measures shall be specified, ranging from the choice of resistant plant varieties and crop rotation to the use of suitable fungicides or other protective measures. The collection of estimates of the incidence of harmful organisms of the observed plants shall contain factual observational data on the occurrence of diseases and pests in various municipalities of Lithuania. Each entry shall indicate the date of observation, the name of the plant, the disease or pest found, the estimate of the damage and the level of damage characterising the intensity of the occurrence, from weak to severe. These data provide an opportunity to analyse the dynamics of the spread of harmful organisms, to monitor geographical differences in their spread and to predict possible outbreaks under meteorological and agronomic conditions. All three data sources complement each other by providing consistent and comprehensive information on the state of plant protection in Lithuania. Pest and disease catalogues provide a detailed context about the biology, prevalence and control capabilities of harmful organisms, and a set of monitoring estimates provides factual data from field observations to assess the situation at a given time. This data structure allows sound decisions to be taken in agricultural activities, timely preventive measures and the implementation of integrated plant protection principles. The dataset consists of data that has been collected and kept up-to-date since 2025, including new observations, study findings and expert insights. Data provider shall mean the Agricultural Agency under the Ministry of Agriculture of the Republic of Lithuania. Additional information, answers to questions and consultations shall be provided on the website of the Integrated Information System for Plant Protection Information, Consultation and Training (IKMIS): https://ikmis.lt.