A fully flexible valve actuation (FFVA) system was developed for a single cylinder research engine to investigate high efficiency clean combustion (HECC) in a diesel engine. The main objectives of the study were to examine the emissions, performance, and combustion characteristics of the engine using late intake valve closing (LIVC) to determine the benefits and limitations of this strategy to meet Tier 2 Bin 5 NOx requirements without after-treatment. The most significant benefit of LIVC is a reduction in particulates due to the longer ignition delay time and a subsequent reduction in local fuel rich combustion zones. More than a 95% reduction in particulates was observed at some operating conditions. Combustion noise was also reduced at low and medium loads due to slower heat release. Although it is difficult to assess the fuel economy benefits of LIVC using a single cylinder engine, LIVC shows the potential to improve the fuel economy through several approaches. First, because of the lower noise and smoke emissions, LIVC offers a promising strategy to expand early premixed charge compression ignition (PCCI) operation to higher load ranges. Second, LIVC reduces CO emissions and improves combustion efficiency at low loads by optimizing the fuel injection timing. The current results show about 30%-50% NOx reduction is achievable depending on the operating conditions and injection strategies if the combustion phasing is fixed. For the same NOx emissions level, LIVC reduces the EGR requirement by 15-25%. A NOx emissions model in Arrhenius form was developed based on the FFVA experimental results. The model does a good job correlating engine-out NOx with intake valve closing time, EGR rate, engine speed, A/F ratio, and combustion phasing. The correlation is used to explain the impact of LIVC on NOx reduction.